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Kyoto Encyclopedia of Genes and Genomes Expression Database

The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. KEGG Databases is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping. KEGG Objects is a computer representation of the biological systems. It is based on the concept of graph for representation and manipulation of various KEGG objects from molecular to higher levels. Mathematically, a graph is a set of nodes (KEGG objects) and edges (biological relationships). Each of the KEGG objects (database entries) is given an unique identifier shown below. Originally, the integration of pathway information and genomic information was first achieved in KEGG by the EC numbers. Once the EC numbers were correctly assigned to enzyme genes in the genome, organism-specific pathways could be generated automatically by matching against the networks of EC numbers (enzymes) in the reference metabolic pathways. However, in order to incorporate non-metabolic pathways and to overcome various problems inherent in the enzyme nomenclature, a new scheme based on the ortholog IDs was introduced replacing the EC numbers. KO (KEGG Orthology) is a further extension of ortholog IDs based on not only the pathway maps but also the BRITE functional hierarchies, most notably classifications of protein families. The molecular interaction/reaction network is the most unique data object in KEGG, which is stored as a collection of pathway maps (graphical diagrams) in the PATHWAY database. Reflecting the map resolution, KEGG PATHWAY is organized in a hierarchy. The top two levels in the current hierarchy is the following. KEGG EXPRESSION is a repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. Sponsors: The KEGG project is currently supported by: -Bioinformatics Research and Development (2006-2010) of the Japan Science and Technology Agency -Grant-in-aid for scientific research on the priority area Comprehensive Genomics (2005-2009) from the Ministry of Education The computational resources are provided by: -Bioinformatics Center, the Institute for Chemical Research, Kyoto University Past supports include: -Grand-in-aid for scientific research on the priority area Genome Informatics (1995) from the Ministry of Education -Grand-in-aid for scientific research on the priority area Genome Science (1996-2000) from the Ministry of Education -Research for the Future Program (2000-2004) from the Japan Society for the Promotion of Science -Bioinformatics Research and Development (2001-2005) of the Japan Science and Technology Agency -21st Century COE Program Genome Science (2003-2007) from the Ministry of Education

URL: http://www.genome.jp/kegg/expression/

Resource ID: nif-0000-21234     Resource Type: Resource     Version: Latest Version


encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis



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12:00am September 21, 2010

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Version 2

Created 3 weeks ago by Christie Wang

Version 1

Created 5 years ago by Anonymous